Align Serine/threonine exchanger SteT (characterized)
to candidate WP_013403835.1 CALHY_RS10010 amino acid permease
Query= SwissProt::O34739 (438 letters) >NCBI__GCF_000166355.1:WP_013403835.1 Length = 436 Score = 313 bits (801), Expect = 9e-90 Identities = 167/430 (38%), Positives = 254/430 (59%), Gaps = 4/430 (0%) Query: 8 LKKEIGLLFALTLVIGTIIGSGVFMKPGAVLAYSGDSKMALFAWLLGGILTLAGGLTIAE 67 LKK + + AL+LV+G +IGSGVF K V YSG FAWLLGG+++L G L AE Sbjct: 7 LKKNLNIWMALSLVVGMVIGSGVFFKATPVAKYSGSFAFIFFAWLLGGVMSLCGALVAAE 66 Query: 68 IGTQIPKTGGLYTYLEEVYGEFWGFLCGWVQIIIYGPAIIGALGLYFGSLMANLFGWGSG 127 + P TGGLY YLE++YG FL GW+ +IY PAI+ AL + F ++++ Sbjct: 67 FSARYPHTGGLYVYLEKIYGNEISFLFGWMNTLIYTPAILSALSVLFADQVSSMLNANQM 126 Query: 128 LSKVIGIIAVLFLCVINIIGTKYGGFVQTLTTIGKLIPIACIIVFGLWKG-DQHIFTAVN 186 + ++ + + + +IN+IG KYGG +Q L T+ KLIP+ II+FGL + + F + Sbjct: 127 VHDILVLSILTAIVIINVIGNKYGGALQLLATVLKLIPLFLIILFGLIRPIEAENFASYG 186 Query: 187 ESISDMNFGAAILATLFAYDGWILLAALGGEMKNPEKLLPRAMTGGLLIVTAIYIFINFA 246 NFG A+L+TL+AYDGW+ + + GEMKN +K L + G+L V +Y+ +N A Sbjct: 187 HFTK--NFGLAVLSTLWAYDGWLSVPNVAGEMKNAKKNLVLVLIFGMLFVIVVYLLVNIA 244 Query: 247 LLHILSANEIVTLGENATSTAATMLFGSIGGKLISVGIIVSIFGCLNGKVLSFPRVSFAM 306 ++++ ++ T ENA + + LFG IG LIS+GII+SI G LNG L+ R+ +AM Sbjct: 245 YINVIGIGKLAT-AENAINLISEKLFGQIGKVLISLGIIISIVGTLNGFALTGIRIPYAM 303 Query: 307 AERKQLPFAEKLSHVHPSFRTPWIAISFQIALALIMMLISNPDKLSEISIFMIYIFYVMA 366 A ++ S +HP F TP + L+L+ + + ++L+++++F +IFYV+ Sbjct: 304 ATNQRFIVNNVFSKLHPRFATPVNSSILVYILSLLYIFTRSFNRLTDLAMFSTWIFYVLF 363 Query: 367 FFAVFILRKRAKGEKRAYSVPLYPFMPILAIAGSFFVLGSTLITDTMSCGLSILIGLAGL 426 F +FI RKR K Y+ LYP P++AI ++L + + + SILI L GL Sbjct: 364 FIGIFIKRKREGKNKEGYNTFLYPITPLVAIFSGLYILVNNIFLNPTDSIFSILITLLGL 423 Query: 427 PVYYGMKKRK 436 PVY+ K+K Sbjct: 424 PVYFLFVKKK 433 Lambda K H 0.328 0.145 0.437 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 649 Number of extensions: 35 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 438 Length of database: 436 Length adjustment: 32 Effective length of query: 406 Effective length of database: 404 Effective search space: 164024 Effective search space used: 164024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory